Stephen Tettelbach, a shellfish ecologist with Cornell Cooperative Extension of Suffolk County, said his group and members of the Peconic Estuary Program are hard at work trying to determine causes for the die-off, which killed 90 to 100% of adult scallops between last spring and fall.

Among the plausible causes are rising water temperatures, reaching up to 85 degrees Fahrenheit in parts of the bays over the summer, and low-dissolved oxygen levels.

“The landings to this point have been very low and it has been an abysmal season for sure,” Mr. Tettlebach said.

The mortality estimates are based on annual population surveys CCE compiles as part of its scallop restoration efforts based in Orient Harbor.

“We go out every spring … before the scallop season starts and we do population surveys of bay scallops, and also predators, at 20 different sites in the bays,” Mr. Tettelbach said.

Those surveys stretch from Flanders Bay to Orient Harbor, the Shelter Island Sound, Hallocks Bay to Northwest Harbor and several spots in between. To determine scallop populations, ecologists quantify scallop density, or the number of live scallops present per square meter. Those figures are then compared to previous seasons, and changes are analyzed.

Ecologists continue to collect samples to determine the possible presence of disease, though Mr. Tettelbach does not think disease is a likely cause.

Kim Barbour, outreach manager for the CCE marine program, said the Peconic Bay scallop is recognized worldwide and CCE has done a lot to keep populations improving. For eight years now, CCE has run a local festival called Shellabration.

She said restaurateurs “sign off” each year on featuring local shellfish on their menus. This year’s sharp scallop decline has prompted them to refocus on oysters.

Ms. Barbour said this isn’t the first time there’s been a shortage of bay scallops. The harvest available for Shellabration has fluctuated: “it’s not always a great year for them. The years that they’re prevalent and readily available, they are featured more on the menus.”

Ken Homan, owner of Braun Seafood Co. in Cutchogue, called this season “devastating.”

“I think opening day last year we got in about 300 bushels and this year we got the equivalent of about five bushels … maybe 10,” he said.

Mr. Homan, who has been in the industry for upwards of 50 years, suspects the scallops may have died before the season started.

“Maybe they spawned early and died early,” he said. “They only have a short life, less than two years.”

This isn’t the first time Peconic baymen have seen such a sharp decline in live scallop populations. While harvests in 2017 and 2018 were reported by local baymen as the best since 1994, some of the poorest years Mr. Tettelbach is familiar with occurred in the mid-’80s and early to mid-’90s.

“In 1994, we had a phenomenal harvest year, with 300,000 pounds, and then the next year it dropped down,” he explained. “ ’95 was the worst brown tide we had and that really just crushed the scallop industry.”

By 1996, the total landings for bay scallops in the state amounted to just 57 pounds, a 99.98% decrease in two years. “That’s the biggest one I’ve seen,” Mr. Tettelbach said, “and I was hoping I’d never see that again.”

The landings of 2017 and 2018 were each valued at about $1.5 million to commercial scallopers, according to Mr. Tettelbach, who pointed out other economic multipliers that emanate from the landings, including the impact on shuckers and visitors, often stopping at shops along the way and boosting the local economy.

The economic multipliers mean that the value of the fisheries to the local economy is well above what the direct harvest generates for the scallopers, he said. “It affects the North Fork, Shelter Island, it affects the South Fork, Riverhead … It is a regional fishery and it’s going to have a big impact on a wide area.”

A limited number of live scallops were found recently in Cold Spring Pond in Southampton and in Three Mile Harbor in East Hampton, but the numbers weren’t significant compared to previous years, Mr. Tettelbach said.

A recent effort to transplant vulnerable juveniles into deeper waters last week quickly fell through, he added, when baymen came back with very few.

Compared to other aquatic species, bay scallops are more sensitive to environmental factors than clams and oysters, he explained.

“It’s getting to where scallops just aren’t able to survive those [water] temperatures … If things get to a dangerous level, the scallops are going to be the first ones to show signs of that,” he said.